Bioinformatics analysis of aberrantly methylated-differentially expressed genes and pathways in hepatocellular carcinoma

Table 5 Modules analysis of the protein–protein interaction network

Category	Module	Score	Nodes	Enrichment and pathway description	Genes
Hyper-LGs	1	10.00	10	GO.0005886: plasma membrane	ADRB1, VIPR1, PTGDR, SCTR, CALCA, GPR83, ADCY1, ADCY5, PTGER2, PTGER4
				GO.0007187: G-protein coupled receptor signaling pathway
				GO.0004016: adenylate cyclase activity
				has04080: Neuroactive ligand-receptor interaction
	2	6.00	6	GO.0051953: negative regulation of amine transport	CCL19, ADRA2B, P2RY12, CXCL6, NPY5R, CXCL1
				GO.0008009: chemokine activity
				has04062: Chemokine signaling pathway
	3	5.68	20	GO.0005886: plasma membrane	OXT, SERPINE1, EDNRB, PTGS2, ADRA1A, IL18, CRP, SOCS3, EFNB3, MMP2, EPHB1, TIAM1, EFNA5, TBXA2R, EPHA2, TLR2, SNAI1, FYN, GNA14, PROK2
				GO.0005003: ephrin receptor activity
				GO.0051240: positive regulation of multicellular organismal process
				hsa04360: Axon guidance
	4	4.50	5	GO.0005605: basal lamina	ITGA9, ITGB8, COL6A2, LAMC2, LAMA2
				GO.0030198: extracellular matrix organization
				hsa04512: ECM-receptor interaction
Hypo-HGs	1	17.56	19	GO.0022402: cell cycle process	CDCA5, KIF14, BRCA1, CENPF, RACGAP1, NEK2, CDKN3, DTL, MCM2, MCM10, CDC45, PTTG1, ANLN, CDC20, RRM2, AURKB, MKI67, STIL, CCNE2
				GO.0015630: microtubule cytoskeleton
				GO.0003688: DNA replication origin binding
				hsa04110: Cell cycle
	2	5.00	5	GO.0007188: adenylate cyclase-modulating G-protein coupled receptor signaling pathway	CNR1, CCL20, ADCY6, HTR1D, CCL25
				hsa04062: Chemokine signaling pathway
	3	4.50	5	GO.0005615: extracellular space	REN, PLA2G1B, TIMP1, MMP9, VWF

Hyper-LGs: Hypermethylated, lowly expressed genes; Hypo-HGs: Hypomethylated, highly expressed genes.